Options For Analyzing Relative Quantification Data; Creating The Study - Applied Biosystems 7900HT User Manual

Options for Analyzing Relative Quantification Data

SDS Multiple
Plate Documents
(for Small-Scale
Analyses)
RQ Manager
Software
(for Medium to
Large-Scale
Analyses)

Creating the Study

Creating a
Multiple Plate
Document
Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide
Applied Biosystems provides two ways to analyze data collected for relative
quantification experiments.
In the case of relative quantification, the SDS software uses a different kind of plate
document, called an SDS 7900HT Multiple Plate Document (*.sdm), to analyze data
from small relative quantification studies consisting of less than 10 plates. Unlike
file-based plate documents, multiple plate documents save the settings and results of
an analysis. Regardless of whether you are analyzing data from a single plate, or
from multiple plates in a series, you must create a multiple plate document to
conduct the analysis.
The SDS software does allow you to open individual relative quantification
Note:
plate documents, however they cannot be used individually to generate gene
expression values.
The RQ Manager Software is a stand-alone application used to conduct medium- to
large-scale analyses of relative quantification (gene expression) data stored on an
SDS Enterprise Database. The software can conduct comparative analyses of over
97 detectors (96 target genes and 1 endogenous control) across 200 plates, or
approximately 153,600 multiplexed reactions run on an Applied Biosystems 7900HT
Fast Real-Time PCR System instrument. See the RQ Manager Software User Guide
(PN 4351670) for more information.
To conduct a comparative analysis of a series of relative quantification plates in a
study, you must first create a Relative Quantification Multiple Plate Document.
1. In the SDS software, click
2. Configure the New Document dialog box with the following settings:
• Assay – Relative Quantification (∆∆C
• Container – the plate formats used to run the samples in the study.
Relative quantification studies cannot compare data from runs
IMPORTANT!
performed using different plate formats (for example, samples run in a 96-well
plate cannot be compared to those run in a 384-well plate).
3. Click . The software displays a new plate document with the appropriate
attributes.
4. Add the relative quantification plate documents to the study as explained in
"Adding Plate Documents to the Study" on page
Options for Analyzing Relative Quantification Data
(or select File > New).
) Study
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